Where is the best place to exchange U.S. dollars in these 2 cities?

There is no need to exchange money - simply pull whatever cash you need from ATMs.

Carrying large amounts of cash with you is not recommended - too many options for loss. And changing cash - at either a bank or bureau de change - will give you a very poor excahnge rate vs what you get from the ATM.

Just returned from Prague, Krakow, Budapest and Vienna. Had absolutely no problem using ATM or Bankomat as they are known there. Money exchange places are everywhere but you really have no need for them.
Have a great trip.

In Budapest, a bank (I think it was Citibank) gave me a better exchange rate to convert Euros into Forints than my hotel did.

actually, in my experience, they give very good exchange rates in Prague for exchanging either cash or TCs to the local currency. They are close to ATM rates.

If you do want to do that, the American Express office gives very good rates (just over the bridge on the Mala Strana side), and any Travelex office has decent rates that I've seen. I imagine smaller companies might not, but I would not guess at these things -- just know what the actual current interbank rate is and compare to what a place will give you (bottom line, of course, I assume you know the different and must find out all charges or rate differences).

Last time I looked, the American Express in Mala Strana (Prague) closed. The main one is on Wenceslas Square. I was in Prague last week, and used ATMs easily.