According to a Lexis-Nexis search for "OPINIONBY(Thomas) and dissent," Thomas has written 50 non-unanimous majority opinions in his time on the court. For comparison, in the same time Souter, a judge of similar seniority has written 63 non-unanimous majority opinions.

Since the year 2000 the number of non-unanimous majority opinions by each justice is (in order of seniority):
Rehnquist: 25
Stevens: 25
O'Connor: 27
Scalia: 16
Kennedy: 24
Thomas: 18
Souter: 15
Ginsburg: 15
Breyer: 15

There has been a lot of stuff over at the Volokh Conspiracy trying to debunk the "Thomas is a stupid lazy idiot" myth which is how I figured out how to do this sort of search, see this post, for example.