Looking at their reigns in totality (30yrs respectively),
Bonanno was far more respected both within his Family and throughout the country. What is not fully understood is that, The Profaci/Colombos were dysfunctional long before the Gallos because of Profaci's greed and he ordered more hits than given credit for. They were probably the most "thrown together" bunch when the Commission organized in 1931. Profaci came from a powerful clan in Villabate (similar to Bonanno) but he was known to be involved in the street fighting of the Castellamarese War. He was kinda "gifted" his organization because of his connections.

Bonanno was more respected (from a street perspective) because of his involvement in the War. Furthermore, you have to look at the 20 or so guys who retired to Arizona with Joe. That says to me, no matter what the narrative is, the man was respected by people.

As far a wealth, Profaci was richer from a legitimate standpoint. But I believe if you combined legitimate and illegal it might sway to Bonanno's favor.