I would have a really hard time choosing between the two shows-I think they're both fantastic.
Sister Act is a fun, fast-paced original musical featuring fantastic turns by Patina, Victoria Clark and Marla Mindelle. I really love the score (I'm a huge Menken fan) and Douglas Carter Beane's book rewrite is very witty.
Anything Goes is a breezy, well-done revival. Sutton is great, and so is Colin Donnell. The choreography is great and the orchestra sounds wonderful.
If I could've only seen one (and, looking in retrospect now that I've seen both), I'd go with Sister Act, probably just because it's a new musical, and I'd always go for something new over a revival, no matter how good either of them are. And, in this case, you're talking about two top-notch productions. I've returned to Sister Act and liked it even better the second time. But I'd return to Anything Goes, too.
"Art, in itself, is an attempt to bring order out of chaos."-Stephen Sondheim