I can’t give specific recommendations but marinas inland in the Netherlands tend to be much cheaper, having only some stagings with water, power and loos. There is a pleasant small YC in Gouda for instance but you’d need to look at a transport map to find one to suit your needs.
As Johnalison says, there is a plethora of small club operated marinas throughout Netherlands. One example we found friendly is Watersportvereniging Ijmond at the junction of Sparne Zijkanaal C and Nordzeekanaal. Quite basic but adequate. Bit too close to Schiphol for noise. Have been told it's cheap. On bus route from airport.
My I suggest getting the Omio app. This gives travel via train or bus - prices and times. Eg from Middelburg to Schipol Airport regular train at c2.5 hrs travel time (with a transfer at Rotterdam) for around €27 one way. It’s a good guide to accessibility anyway.
I was based for a few happy years at Amsterdam marina. Very convenient for Schipol and a brilliant destination. But your boat will go green in winter and will get dirty. It doesn’t freeze up in winter - even when the small canals in the city have skaters on. Expensive by Dutch standards, cheap compared to UK. I’d go back again but times have changed.
Middelburg is a nice place and cheap for long term berthing from what I’ve heard. Plenty of options available throughout the Netherlands.
Agree on the friendliness of Watersportvereniging Ijmond. Always welcoming when we have stopped there. We know people who are members also, and they're happy. Not strictly within your criteria but a relatively simple day (just under 40 miles) from Ijmuiden through Amsterdam and the Markermeer, we keep our boat in the Grashaven in Hoorn. Direct train from Schiphol (45 minutes or so) then a 10-15 minute stroll through town - which is useful for provisions. Or if you're by car, ample parking. Plenty of boats stay in the water all winter. Good facilities, reasonable prices. Worth a look if you don't mind being a little further inland (going the other way it's a similar distance to Den Helder).
Oostende, Mercator Marina. Totally sheltered behind the lock. Oostende airport 15 minutes by bus, Brussels airport just over an hour by train. Train and bus station next to the marina.
I'm a bit late to the party, but I would suggest Kokernoot in Zaandam if you're looking for a berth in (almost) Amsterdam. I think it's probably the cheapest in the area. There's a bus station about a 10 min walk away with connections to the city, etc.