Lee, McClellan and Fremont were all offered Major General of Regulars. The ranks were to conform to their then seniority on the Army List.
Now, in the US Army of the time seniority was a weird (to my eyes) thing. It was based upon the date of promotion to Field Officer, which fixed your place in the Army List. Now, by a strange series of events, McClellan was senior, since Lee was still a Captain (Bvt Maj, which didn't count) in 1855 when McClellan was Commissioned Major of the 1st Cavalry (Lee was Commissioned Lt Col of the 2nd Cavalry later that year).
Fremont was senior to either of them, having been promoted Lt Col in the regular Army in 1847.
All three would have been promoted Major General of Regulars on 14th May 1861 (when ALL the offers of promotions etc. were actioned). The Commissions would have been handed out in order of seniority on the active list, Fremont, McClellan, then Lee.