Boston is not a hub for any airline so the question should be which airline has a hub which is on route of the destinations you and your wife fly most. If you fly a lot to the west coast United, AA or NW could be ideal for you with its ORD or MSP hubs. If you fly South a lot United or Delta with IAD or ATL. Continental with its hub in EWR is a choice, too.

Other idea would be to join a Skyteam airline so you can earn miles on CO, NW and DL. In this case maybe Delta because I think Boston is a focus city of Delta if I'm right.

My recommendations are only to help you to get an idea on what base you could choose a FF program and not final.