Yes, I gather St. Anthony's got a new rector a couple of years ago, and immediately started hurtling into the abyss. Until then, they were pretty good. (The Paulist Center was always weird, IMO -- at least as far back as the 60s.)
An absolute *GEM* that I found years ago is the St. Thomas More chapel at 49 Franklin St. - maintained by the Propagation of the Faith. It's between Filene's and the old Woolworths (TJMaxx now I think) building, on the Filene's side walking towards Post Office Square -- a couple of buildings behind Filene's.
The other wonderful 'stop in chapel' is the one at the Pru on the bottom floor, St. Francis - kind of modern, but very, very orthodox. Excellent little bookstore as well. It's staffed by the Oblates of the Virgin Mary.