Standard letter for 5-methylcytosine
Well, don't use M or B, those are already taken (C or A, and not A, respectively).  You can see the full list here: http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html (The enWiki article on Nucleobases lists a few others but I would ignore those as 1. D is present in both and 2. they are rare and inapplicable)

5-methylcytosine isn't on there.  If you want to be pedantic about it, 5-methylcytosine is an epigenetic marker and as such is by definition not a genetic sequence; that remains simply a C and, genetically, the sequence is the same, despite the fact that it may indeed make a difference.

Most of the time people use m5C, so I'd go with 5 if I were you.  That certainly isn't used for anything else and if you must use a single character most anybody will know what you are talking about.