Planning a trip with my husband and 12 yr old son. I'd appreciate any feedback on Wyndham Boston,Omni Parker House,Eliot Ste Hotel. For a 1st timer, would I be better off staying in Back Bay/Copley or Downtown/Wharf area? Plan to walk/use T, to take in museums/historic, everything fun or quirky(not really here to shop).

I'd recommend the BackBay/Copley area rather than downtown or waterfront. You're closer to more things to do and handier public transport. Plus, the waterfront area can be mighty cold and windy in winter! Parker House isn't a bad location, though, and a very historic place itself.

We were there last year right after Christmas. Stayed at Omni Parker. Even though their website claimed they had extensive renovation, our room was pretty tired. We asked to be moved and they claimed most of hotel was sold out, even though it did not appear to be full. Next time we will stay at Westin Copley Plaza. Good location. It is true about the wind & cold, bring lots of clothes for layering!!!!

Agree with BackBay Copley area.
Things to do besides museums, (Science with IMax theatre, Museum of Fine Arts, etc.: Nutcracker Ballet at the Wang Center, Holiday Pops at Symphony Hall, lots of other "seasonal" happenings. Get the Thursday Calendar section of the Boston Globe. Lots of helpful ideas.
If you are here (I am in Boston) close to New Years there will be preparations for First Night with Ice Sculptures in the Boston Public Garden.
It is likely to be cold and windy. Be prepared.

Of the three hotels you mention, I understand the Eliot Suite is far and away the best one. Location isn't bad at all (Back Bay) and the rooms are supposed to be wonderful (I know a family who has stayed there and loved it). It's just a block or so to the nearest T, and close to Newbury St. The Pru, etc. Great location, great hotel.