Nusach Askenaz says Baomer, Nusach Sefard and Sefardim say Laomer - Why does everyone call it Lag Baomer - why not call it Lag Laomer?
The Lubavitcher Rebbe zt"l writes that there were halachic and kabbalistic reasons to switch from בעומר to לעומר in the counting (as discussed in the commentaries to Shulchan Aruch, Orach Chaim 489:1). However, there was no real need to be so particular about dates and the like, so the older form was retained there. (This is similar to what Curiouser wrote in his comment, although slightly different: according to this approach, had the older version for counting indeed been היום יום אחד לעומר, etc., then we probably would indeed call it Lag Laomer. Indeed, I believe some Sephardim call it thus.)
In another letter, the Rebbe cites "sefarim of Polish [Rebbes]" - he doesn't specify which ones - who point out that ל"ג בעמר is equal in gematria to משה.