Here is a few that come to mind
Vinnie Rossi LIO is wonderful and the phono stage is really good not to mention a whole host of other options as you build it as you need.
Luxman integrated's have a fine phono stage
Acuphase may still have a MC section as an option.
Can't think of any current tube integrated's with a phono stage but i'm sure others will chime in as some have already.