The treasurer is not the comptroller's boss, BUT, the treasurer is the person who authorizes the payment of state payroll. When the State of New York works off of emergency appropriations, when there is no budget in place, the checks are held by the State treasurer and released upon their orders. You might recall that State legislators do not receive their paychecks when the budget is late because the release of checks can not happen unless the treasurer first directs the comptroller to release them. Sans the budget the treasurer has not authorized the release of the checks, even though the comptroller wished to release them. In fact, they are kept in a safe that can only be opened by the treasurer.
State employees paychecks during a budget crisis have in fact been driven by employees of the state treasurer to district offices at the last minute to make sure salaries were paid as soon as the emergency appropriations were authorized.
No, I'm no fan of the comptroller. I've seen the results of his bull$hit audits that are politically motivated and no less than witchhunts. Yes, check the value of the pension fund today as opposed to last summer, prior to 9/11. You'll see its off a few hundred million, perhaps more, if I recall correctly.