Johnny Unitas was the best QB in Colts history because he was inducted into the hall of fame in 1979. He was a 10-time Pro Bowler and 5-team First-Team All-Pro. He threw 40,239 yards and 290 touchdowns which are records in the Colts team history. Since this question is asking for an opinion than you have to mention one other QB, Peyton Manning. Since he is still active his career numbers are not really up there with Unitas's, but he's a 3 time MVP and a Super Bowl Champion. When he retires he will certainly go the HOF and will certainly be considered one of the best QB's of all time.
John Mackey was a very impressive tight end for the colts but played in a different era. I don't know if I have a descrete answer right now, but I think when his career is over, Dallas Clark might own a majority of tight end records for the colts and will have to be at least in consideration if not in my opinion the best TE in colts history. He has already set colts single season records with touchdown receptions and yards.
Jack Trudeau started 11 games at QB and Gary Hogeboom started 5 games at QB for the 1986 Colts. Blair Kiel was third string.
QB Dan Orlovsky
John Elway
Earl Morrill was the Colts starting QB. John Unitas replaced him in the 3rd quarter and led the Colts on their only scoring drive.
Peyton manning of the Indianapolis colts
peyton manning #18 Qb
Even though he was originally drafted by the Blatimore Colts and didn't really play that many games for the Indianapolis Colts QB-Art Schlischter.
Peyton Manning.
Jim Harbaugh was the starter and Paul Justin was the backup. Kerwin Bell also saw action at QB for the 1996 Colts.
Earl Morrall (9 starts at QB) and John Unitas (5 starts).
Jeff George started 12 games at QB and Jack Trudeau started 4 for the 1990 Colts. Joe Ferguson and Mark Herrmann were backups.
In the NFL, both Eli Manning of the Giants and Peyton Manning of the Colts were sacked 16 times, the fewest of any starting QB for the 2010 season.