Best upgrade to my Nikon D90?

Your 70-200 is likely NOT a DX only lens. Which one is it? That would be my go-to lens for pets and kids when not shooting wide.

If you've got the money, the D800 seems ideal. But you might be just as happy with the D7000 and the lenses you've already got.

I'm sorry I was mistaken, it's a 50-200mm VR DX.
The D800 seems great but I can't find any good information on the low light performance. Snapsort says low light performance is unknown?

The D800... I'd wait to see reviews on high ISO noise. The logical step up from a D90 is a D7000, but my advice would be to first examine your technique closely - turn off auto D-lighting (it adds noise at high ISO) and make sure you're nailing exposures (bad exposure adds far more noise than a previous generation sensor). Don't use the 18-105 lens in low light. The D90 is actually a very good low light light performer. You can get some improvement by going to a new camera, but it's an incremental improvement, not a miracle cure.

If you do stick with DX, an f/2.8 normal zoom is a good choice for lower light. Sigma and Tamron both make affordable ones with VR. You can shoot great portraits with your 70-200mm lens on any camera.

Oh, 55-200mm DX? Your best portrait lens currently would be your 50mm. The equivalent to the 55-200 for FX is the 70-300 (the Nikon VR version and the Tamron VC version are both good). The D800 low light performance is unknown because there are so few D800's floating around and nobody who does quantitative tests for that has done so yet.

Thanks for the tips. My husband stole my camera and took it to work today :( but I will check on the D-lighting when he comes home.
As far as exposures... I just dial up or down based on how it looks to me. I should probably be using the histogram more but I'm trying to go quickly especially now that she's moving around more. If I fix exposure in Lightroom will it add more noise to the edited image? That might be a stupid question... haha :)
I bought the 50mm with the intention of taking better portrait shots but I have trouble because while I love the wide aperture it's almost like I don't have enough focal points on the D90 to ensure good focus (it has 11). So I might have like one eye in focus and the other one not in focus if I'm shooting at an angle. Or if she twitches a muscle it's suddenly her forehead in focus... ugh.
Do you think the 51 focal points on the D700 is a good selling point?

Jessica... if FX and good video are a must the answer is D800. It seems that D800 is equal in low light with D700 so apart of the very expensive D4 there is nothing better on the market. Looking at your type of photography I'd think that instead to invest so much in a body that in a few years will loose its value, you better go with a DX setup like:
D5100
Tamron 17-50/2.8 VC
Nikon 50/1.8 AF-S
Nikon 70-200/2.8 VR I - used
This whole setup cost probably less than a D800 and a D800 needs desperately good/expensive glass that will raise your bill a lot.
My reason is that D5100 is the best DX camera for video, its movable display its a plus for this and the IQ of its sensor si equal with that of D7000, performing very well in low light / high ISO.
Also investing in good glass is more important in long term than investing in state-of-the-art bodies.

Well I think the good video (with autofocus) is what is gonna sell my husband on this purchase :)
My understanding is that the D5100 is only slightly better in low light... not sure it's worth the upgrade.
I thought I had a fairly decent set of lenses for what I wanted to do but since I'm still finding noise and getting poor focus I felt like a new body was the answer... I don't know. It's confusing! :)
Priced as it is now the D800 is a way better deal than the D700 but I'm wondering if D700 will go down significantly.

Nice photo, but according to the EXIF data it was shot at ISO 1100 so I would expect some noise. Sure you might get less noise with of the cameras you mentioned, but this seems rather a lot of money to spend just to reduce some noise. How about spending a lot lot less money on an SB700 and bouncing the flash, thereby reducing your ISO to 200 and vastly reducing noise.
With regards to the video, again the cameras you mention are a lot of money to get HD video with AF. Maybe you could consider a dedicated camcorder for a fraction of the price.
I would also consider an 85mm prime . I use my 50 and 85 1.8's with my kids (2 and 7) on my D90 quite a lot and love the 85.

I am somewhat in the same situation as you with my D90 although I am not looking at a FF body. I will wait a few more month to see if the rumored D400 comes out, otherwise I might go for the D7000. At a native 64,000 ISO it is quite good.