which is a better location

don't want to be to far away from the sites and want to be able to walk to small restaurants and food places since we will be doing some eating in.

The impression of the St. Peter's area that I have is of a fairly institutional neighborhood oriented to religious business and visitors. Trastavere is more youthful and lively.

connie,
I think you will find Trastevere a better location. Around ponte Sisto will be closer to the places most tourist want and I think the restaurants are better in the Trastevere area.

I would say Trastevere. The Vatican is pretty far out from the main tourist sites while you can walk almost anywhere in central Rome from Trastevere.

Both Vatican and Trastevere are on the opposite side of river from the bulk of visitor sites. Trastevere is perhaps a bit closer. Regardless of mode of transport, foot, taxi, bus or tram, you must first get to the river, then to a bridge, across the bridge, and then on toward destination. This adds time and distance. We liked Trastevere, staying in that zone 3 nights. More interesting (except for major sites) than east of Tiber.