Actually Mike Markkula was likely the CEO. At the time, Jobs was largely running the company.
Here is the list of CEOs of Apple.
Michael Scott 1977-1981
Mike Markkula 1981-1983
John Sculley 1983-1993
Michael Spindler 1993-1996
Gil Amelio 1996-1997
Steve Jobs 1997-2011
Tim Cook 2011-Present
Some software work w/Microsoft:
1977-78: Applesoft Basic
1980: MS SoftCard allows Apple II users to run CPM/80 apps
1981: Sneak Peak of the Mac given to MS, they begin developing products for it
1984: MS Basic, Multiplan, File, Word, Chart and Excel for Mac
It looks like all the initial work between MS and Apple took place under Mike Scott & Mike Markkula. System 7 8 and 9 were mentioned and those are all at least 1991, so those would be John Sculley. You are right tho TBell, Jobs did run a lot of the company no matter who was the CEO at the time. He and Sculley were joined at the hip and Markkula and he always seemed to be working together very closely as well. At least from everything I have ever read, including the Jobs bio.
BTW, I pulled those software dates from this page: http://www.thocp.net/companies/microsoft/microsoft_company.htm