I can't see any way that a clip-on mic wouldn't be in the way, so I think free standing is the way to go. An SM-57 will work fine if you're playing it on stage, and if you just want to record, I'd strongly consider the EV 635A. That second one is an omni, so less suitable for stage.
A microphone in front of an acoustic will have a different sound than a pickup on an electric. The choice between them depends on what sound you're looking for.
LoPrinzi Model B tenor (cherry)
Cordoba 20TM-CE tenor
Oscar Schmidt OU53 baritone
Makala Dolphin (thanks Chap!)
Many and various bass guitars