Is it the kind of program where you'll definitely finish in 2 years unless something bizarre happens? Will you graduate before June 1st of your matriculation year?
If so, you'll be fine applying during the last year of your MS. If it's a thesis based program where end date is more flexible...be careful. MD/PhD acceptance will likely be contingent on completing your MS on time. That was the case for me, and I nearly drove myself insane trying to finish my MS thesis/defense before matriculation.