Since Mainz and Wiesbaden almost blend into each other, Rudesheim is pretty much equally accessible from either. I prefer Wiesbaden, but probably just because I've stayed there so often.

I recommend the Hotel de France on Taunusstrasse. Reasonably priced, and if you have a car they have a parking garage for a relatively modest daily rate, but there is also a public garage fairly close by. (Parking can be difficult in Wiesbaden). The included breakfast is fantastic and they are very nice people.

It is not terribly close to the train station, but nothing I'd recommend (except possibly the Crowne Plaza) is. If you have a regional transportation pass that will be good for the Wiesbaden buses, and the number 1 has a stop directly by the hotel and the number 8 is about 2 blocks away, both run frequently and drop you off right outside the train station.