Two things I'd suggest is don't build the maximum level of farms(i usually only build the first level) and demolish granary biuldings when you reach large city size this helps to prevent those 40000 people cities, stay clear of Lantifunda as well unless its for the reforms.

Also if your so flush with cash give it away to other factions to help along your intrests in other areas of the map.

Large garrisons can help control the cash flow as well, in a fully developed city i would usually have 6 units on garrison duty, more if it was vulnerable to attack.