Comfort Inn
Americas Best Value Inn
La Quinta Inn & Suites
Holiday Inn Exp
Edited to add: Best Western
These are all fairly new hotels with the La Quinta and Holiday Inn built in the last two years or so. (I remember the Holiday Inn was under still under construction and took some damage in Ike - so since 2008) and the La Quinta was started after that. But these two are the closest to the railroad tracks and the Alvin tracks are extremely busy. There is not a whole lot to do in Alvin, so if you are looking for adventure, you might consider looking in the Webster/NASA area. But there is a Casa Ole and Chili's nearby as well as several local sit down restaurants. There is a Sub-way, Taco Bell very close as well as McD and Jack in the Box a little further out.
Edit to add:
I should add, the hotels look clean from the outside - I haven't actually stayed in any of them.

gwashorn has had a cousin stay at the Rodeway Inn. Also fairly new, but located on Hwy 6 surrounded by commercial property.