Im finishing out the 3rd floor and planning on hiring someone to do electric and put hvac as well. The company I contacted does both hvac and electric work. They said they would be wiring a 6 gauge wire from main breaker in garage to 3rd floor and they will put new subpanel in 3rd floor. From subpanel they will wire the new hvac unit and electric for 2 rooms and 1 bathroom. Does this sound like a reasonable plan that would be up to code? Anything I ahould look out for?

It sounds reasonable. That HVAC unit; is it just for the 3rd. Floor? Is it a gas fired unit?
Heat pumps and air conditioning units require a bit of power. If it's just a small unit for the 3rd. Floor you should be OK. As far as adding the sub-panel... that's a common way of adding circuits ot a previously unused / unfinished area.