In regard to Rotterdam, it's a great place to base yourself a little longer if you want to explore some nearby areas like The Hague or Kinderdijk. For Amsterdam, the Jordaan and Nine Streets areas are great, but likely will be the first areas to book up because they are so popular. Also, you'll pay more to stay in these neighborhoods because of the demand.
I also disagree with the comment on De Pijp. It's a great neighborhood with decent access to tram lines and is walkable to Museumplein in certain parts. I recommended De Pijp to a friend who was going to be in Amsterdam part of the time I was there. She booked a 3BR Airbnb on Van Woustraat a block from Sarphatipark while I stayed in a hotel near Museumplein. She loved the location - tons of restaurants, the Albert Cuypmarkt was right there and she found it very safe for her and her 2 teens even when they were out late at night.
Other neighborhoods I would highly recommend are Oud West or Helmersbuurt. As you are looking for a 2BR 2BA for a decent price, you'll find your money will get you a bit more space here. Both are solid neighborhoods with plenty of restaurants and shopping plus decent tram access.
Do consider that many Airbnb rentals are walk-ups and if you (or your colleague) aren't packing light, try to find something on a lower floor. I had another friend who traveled to Amsterdam while I was there and she found herself a really lovely 1BR with it's own rooftop deck that was only about a 5 minute walk to Museumplein, but it was a 5th Floor walk up with some seriously steep and narrow stairs.
Don't rule out separate rooms in a hotel if you can't find an Airbnb. Conscious Hotels has several locations that are generally very reasonably priced. I've stayed at the one near Museumplein. Ibis and Ibis Styles are also ones to check for rates. Their single occupancy rooms may not have the charm and character of an old canal house hotel, but you'll each get your space, free WiFi and a comfortable bed to sleep on. Do a search on Booking.com to see what is in your price range for both hotels and apartment rentals - you can always book directly if you don't want to reserve it through Booking.com.
If not Haarlem, Utrecht can be a viable alternative to base yourself out of with cheaper hotels. You can easily train into Amsterdam as needed and Utrecht is a beautiful city with lots of canals and lively nightlife/restaurant scene.