I've been using my current D3100 for about a year and a half and I am beginning to feel a bit limited with it. I was looking for a camera with better high ISO performance, an in body focusing system, a more durable body (not that I've had any problems), and especially more external buttons! If it can meter some of my old film manual focus lenses (AI-S) that would be a plus as well! I tend to dabble in all different areas, but have been doing a lot of night photography lately. I also really like the U1 and U2 options on the 7000
I don't tend to use the continuous shutter mode at all, so the fps rate is pretty low on the priorities. I've also never felt limited by the 11 point AF on the 3100... but maybe more is better?
At this point I'm looking to spend less than $1k, but may save up a little longer if the D7100 is THAT much better. So is the D90 worth buying over the D7000 at this point given my needs? Any advice is welcome
The D90 is older than your D3100 and has only slightly better high ISO performance. While it has an AF motor built into the camera body it does not support metering with MF (AI) lenses that do not have CPU chips. Both the D7000 and D7100 have better high ISO performance than the D90 and they support metering with MF (AI) lenses.
The D7100 was just released therefore in is the current state of the art. In addition to more resolution, the D7100 has slightly better high ISO performance and color bit depth than the D7000. It also has better and more sensitive AF module. The D7000 is more than likely no longer in production though it has slightly better Dynamic Range than the D7000.
You seem to want to change for some very valid reasons. While, if high-iso performance were the sole determinant, I would buy the 7100 after waiting for the dust to settle, I think there's a little more to the question. The 7k is most like your 3100 in pixel density so, presumably, you already know how to shoot a 15Mp camera. The 24Mp sensor in the 7100 may take some getting used to, especially if you gravitate toward large prints. The necessity for first-class lenses, reasonable shutter speeds, larger apertures and reliable camera support increases with pixel density.
I can't speak to the D90/7000 question directly. I can say that, having acquired a D600, my D90, which I shot enthusiastically for four years, hardly comes out of the bag. The new technology is just that good. I have not yet decided but I am considering a move to the D7100 for a DX complement to the D600.
In defense of the D90, I don't feel it presents much of a problem metering with a manual lens. For instance, I have a wonderful OM-system lens adapted for F-mount. There is zero communication. But the green focus confirmation dot works and exposure is easy enough to determine after the fact with the histograms and highlights display (blinkies). Just so with several other Nikkor manual lenses. The fact you don't concern yourself with frame rate suggests your usual subjects are not so very dynamic as to demand immediate metering.
That said, buying a D90 rather than a D7000 seems to me to be locking in a heftier set of restrictions on your shooting. The analogy of willfully restricting oneself to the right lane for a long trip on a three lane interstate comes to mind. Or, more locally, shall we say, the middle lane of the Mass Pike.
Guess I'm late to the party on this one... but you bought the camera I was going to suggest.
I'm still new to the DSLR environment however, when I got my D90 I was told to do what I could to purchase a D7000. Between the $400 higher price and my ancy-ness when it comes to buying things I pulled the trigger on the D90.
With that said I thoroughly believe I still have a lot to learn to from my D90 but the biggest detriment to it as a camera is it's age. Technology has improved a lot in the past few years so the 7000 is most likely the way to go.
It seams I am late with my suggestion as well, but maybe it will be of use to somebody else having the same question. D90 is a great camera with good ISO performance and D7000 had slightly better ISO performance. D90 can be purchased for a very low price now. My D90 with 30K clicks with Nikon battery grip went for just over $400 I have seen deals for D7000 going around $750 with a kit lens. So the choice depends on the money available. If night photography is what the camera will be judged on, another choice is a used D700. It is a full frame and ISO performance on it is just insane! It broke my fear of ISO above 800 and I am regularly sorting up to 6400 ISO. If you are willing to wait for a deal, you may get D700 under $1200.