For the visa entrance fee to get in, you must pay in euros, US dollars, or GB pounds. Not Turkish lira or any other currency. At the moment, you're best off to use US dollars, since you'll actually pay more in either of the other currencies.
For entry fees to museums or sites, it's Turkish lira only, of course.
By the way, as of this January there is a new Turkish currency being phased in. If you are going before then, you should spend down your "old" Turkish currency before you leave to avoid the hassle of trying to turn it in before the deadline when it becomes worthless. (I forget exactly when that will be, but it is usually within a couple of years of conversion.)