Hi Reinz. When it comes to astrophotography, the mount is pretty much the most important thing. Most astrophotographers who have even moderately diverse goals (i.e. just galaxies and nebula) are going to need to use multiple telescopes with different focal lengths, or at least one telescope with barlows and focal reduces, to get a field of view wide enough or narrow enough to frame their subjects properly. A good mount can last you for many, many years, where as telescopes (or, for that matter, camera lenses) usually come and go until you hit the real high end (i.e. 20" RCOS or PlaneWave telescopes).
For $1000, you can get yourself an entry-level mount. Something like the Orion Sirius, which is the little sibling of the Orion Atlas. The Sirius has a capacity of 30lb, which for visual is generally fine, but that pretty much equates to 15lb for astrography (the Sirius doesn't have the most sturdy tripod, so you REALLY have to stick to the 50% capacity limit for imaging work). That is practically nothing in terms of capacity, but if you just stick to your DSLR and lenses, it'll at least get you started.
The Orion Atlas is a much more capable mount, it's capacity is 40lb, however imagers have been putting on 60-70% of the capacity and getting excellent results. Visual observers have put over 50lb on this mount when using sturdier tripods or full blown piers. The Orion Atlas is $1499, however it's fairly frequently on sale for $1399, and at times has been as low as $1200. Given how important the mount is, especially if you think you might want to move up from your lenses to a real telescope at some point in the future (and entry cost for telescopes can actually be pretty low...for example, the Astro-Tech AT6RC, a 6" Ritchey-Chretien telescope, is only $399 and it's designed specifically as an astrograph.) If you can muster it, I highly recommend getting the Orion Atlas mount, even though it's more than your $1000 budget. It will give you LOTS of room to grow in the future if you find that you like astrophotography (it could even be "the" mount you use for the next ten or twenty years....many people used the predecessor to the Atlas/EQ6 class mounts for about that long.)
From your existing equipment, the 5DIII hands down. Don't use a Nikon for astrophotography...their nickname in our community is "Star Eaters", since they clip
to the black point, rather than using a bias offset (one of the many ways Nikon "cheats" their way towards cleaner shadows
.) Canon's use of a bias offset is the reason there is a lot of banding in their shadows, which isn't good for regular photography. However since in astrophotography we use bias frames to remove the bias from the signal, Canon DSLRs are actually a lot better...they preserve more stars and deep nebula detail. So definitely use the 5D III.
You have a good range of lenses as well for "wide field" work. The 40/2.8 @ f/4 and 50/1.4 @ f/3.5 are both excellent for "whole constellation" images (for example, you could image the entirety of the core Orion constellation, as well as most of his club and kill: http://bit.ly/1lF7hSp
) The 100mm Macro @ f/4 is a great lens for imaging entire small constellations, or for imaging parts of larger constellations (for example, it would neatly encompass the core of Orion, but not his club or kill: http://bit.ly/1jIciah
) The 70-200 at 200mm @ f/4 is great for narrower regions, small constellations (for example, 200mm would encompass Orion's Belt and Sword, and the small reflection nebula M78: http://bit.ly/1mOwpGH
) The 100-400 at 400mm @ f/8, while a bit slower and probably requiring more equipment (such as a guider, which itself would probably require a number of additional accessories to properly mount next to your camera), is good for imaging nebula themselves (for example, it would encompass just Orion's sword, which includes Orion Nebula (M42/M43) and Running Man Nebula: http://bit.ly/1ltmAeo;
or it would encompass just Orion's Belt, which includes Horse Head and Flame Nebulas, IC434, and a number of small reflection nebula: http://bit.ly/1dSzPFJ
If you go with just the mount, you will be able to attach your DSLR and a lens. The 100-400mm is probably not quite going to work, as you would need pretty steady tracking to image at f/8...that's pretty slow. Were talking 1" (" means arcsecond, ' means arcminute, 60 arc minutes per degree) tracking, which is not easy to achieve. So your probably going to be stuck at 200mm and less until you decide to upgrade. Thing is, that is really the best place to start anyway, as at those focal lengths, tracking error is really forgiving, so you should be able to track for several minutes, maybe as much as five minutes, without appreciable star elongation or trailing, allowing deep exposures of wide regions of the sky (which, during the two times of year when the milky way is up, are PACKED with IMMENSE swaths of nebula).
Unguided imaging is basically the domain if the wide and ultra wide field. If you want to see the kinds of images you can get at those scales, you should check out AstroBin. Plenty of good examples there (better than anything I've done as of yet.)
If you get an Orion Sirius mount, which is $1000, then that will suffice for DSLR with 200mm and less. You'll need to get a better mount than that if you want to do more. There are a lot of small APO refractors on the market, ranging in price from around $500 to as high as $10,000 or more, however most of the smaller, lighter ones that would work on a Sirius fall into the same general focal range that you already have with your Canon lenses (200mm to ~800mm). The logical upgrade for you would be to eventually move to a Cassegrain type OTA (Optical Telescope Assembly). Cassegrains include your standard SCT (Schmidt-Cassegrain Telescope), the Celestron EdgeHD (an Aplantic SCT, designed specifically to support a wide and flat field, right into the corners, for imaging), and the Ritchey-Chretien cassegrains (primarily those from Astro-Tech.) Meade also makes some Aplantic SCTs like Celestrons, however they tend to be more expensive, despite not really offering anything more, and there is one special benefit to the Celestron EdgeHD OTAs: They support Hyperstar, a special conversion mod that allows you to do ultra wide field imaging (~200-400mm) at f/2 (REALLY FAST...you could get really deeply exposed images in a couple minutes at that aperture.)
Generally speaking, the best upgrade from DSLR+Camera Lens imaging is to move to something like the Celestron EdgeHD 8" SCT, or the Astro-Tech AT8RC 8" Ritchey-Chretein. Both are reasonably priced, although Astro-Tech's prices are really hard to beat for the quality, optical design, and overall capabilities for imaging. For either of these, you would really want at leas the Orion Atlas (or the equivalent from Celestron, the CGEM or CGEM DX, however the Atlas is really the better option due to the rich community, EQMOD, and the option for installing belt mods to improve tracking and guiding accuracy down the road.)
My recommendation is pick up the Orion Atlas EQ-G, and use your 5D III and 50mm, 100mm, and 70-200mm lenses. You should be able to just bolt your camera to the included Vixen dovetail that comes with the mount, and not bother with purchasing any additional accessories initially. You will need to learn how to polar align the mount (the Atlas comes with a built-in polar finder scope, which once properly centered (the most annoying thing you will ever do, but thankfully you only have to do it once!
), is highly accurate and easy), and you will need to either learn how to use the hand controller to "Align GOTOs", or purchase a $40 EQDIR cable, use EQMOD, and completely computerize your process (HIGHLY recommended, you can buy BackyardEOS ($50) to greatly simplify your imaging sequences, and gain a lot of powerful features, such as highly precise live view focusing on your laptop or a windows 8 tablet, to get the best results.)