The inheritance for Shevet Levi may shed an interesting light on this question.
Historically, there were originally more Leviim than Kohanim, but nowadays in most shuls it seems to be the reverse.
I was once told two possible answers by a HS rebbi:
1. The cynical answer: Leviim are less motivated to pass down their mesorah to their children becasue being a Levi is less prestigious than being a Kohen, so many leviim have been "lost" this way and don't know their identitiy.
2. The geographical answer: The Leviim were spread out in 48 different cities and so less survived than the Kohanim who were concentrated near the Bet Hamikdash.
The Halukah in Yehoshua gives support to answer 2. Of the 48 Levite cities several of those cities were given specifically to the Kohanim. As pointed out by Daat Mikra, all of the Kohanic cities were in the Southern part of Israel, within the tribes of Yehudah/Shimon and Binyamin. This was done prophetically or on purpose because the Mikdash would be in that part of the country. (Also hinted at in V'zot Habracha.) Of course after the exile of the Ten Northern Tribes, the Southern area/Tribes were all that was left.