We just finished a river cruise from Budapest to Amsterdam. We chose AMA Waterways - all excursions, up to five at each stop, were included, bike tours, tasting tours, city tours, architectural tours, etc.
We are normally RS type of travelers, but hubby wanted a pampered experience this one time (after years of caring for elderly parents locally, we were kind of worn out). This was it - in spades. Excellent food, immaculate cabin, kind and wonderful staff. Only 90 travelers on a boat that held 150. Yay!
We booked 3 nights at the centrally located Hotel Oktogon in Budapest (thanks to rec from Mr E above, go to Hungary forum and absorb all his great ideas!). did you know that over 65 travels free on all metro/trams/buses in Budapest? Using google maps, we easily planned our days there. We booked a jazz club with gypsy performers and an Opera performance for 2 of our nights. Took a "free" tour from a local Hungarian, visited the Central Market, wandered and wandered. Rode the 2 Tram just for the scenery. Ate at authentic local restaurants. We loved Budapest!
Also booked an Airbnb in Amsterdam. We had been to Amsterdam before, and we also rented a tandem bicycle to get around while there. Amsterdam was ...very crowded. Although we enjoyed it, we saw a pickpocket event within 2 hours of arrival, our Airbnb was way overpriced (but I understand every accommodation is, with a 26% hike coming soon).
Since it was June, the water levels were too low to continue, so one week was on one ship, the second week we bussed from Regensburg to Nuremberg for our excursion, then a short hop to our "new" ship - identical to the previous ship and expertly handled by AMA - even down to getting the same room number and walking aboard and right to our cabin. Some have had worse experiences (like 2-3 days at same port), but for us it was not a problem, other than having to repack once during the 2 weeks..
We felt extremely safe the entire time (especially Budapest on our own). We were careful in Amsterdam but no problems overall. Went to some great restaurants in both cities, in Ams we took a canal tour (choose carefully, some are better than others), and visited the Rijks museum (we had already been to the Van Gogh, both recommended). One of our days in Amsterdam we rode the bike along the canals leading out of the city, had lunch in a nearby village, a great break from the crowds.
Suggest some cafe stops on your own, for lunch and beer (boy they are very serious about their beer in these towns!).
You will love this trip!