Op I’m another MK resident and while it gets a lot of stick it’s a great place for a break with kids. I reckon that you might find that you could end up wanting to stay longer (not that I’m biased 
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I haven’t been out much to know what’s currently / soon to be open so will list what is normally available and you’ll need to check when you know dates!
Obviously Bletchley Park and TNMoC are both great. Both usually have events through the year so check their websites - TNMoC used to run fab sessions for kids during holidays - sometimes free (well included with admission price) or sometimes with a token fee of say a fiver - Lego mindstorm(?), all sorts of coding or electronics things, code breaking and more - sound like they would appeal to your kids.
MK Museum is also brilliant as mentioned - but really hands on so not sure how they are coping with covid. Loads of things to interactive - old fashioned shops, vehicles to clamber over, a phone and phone exchange collection which sounds dull but is great fun and really difficult to get kids out of, a Victorian parlour with loads of games and instruments to play, a Victorian Schoolroom to tryout, a Victorian kitchen where you can toast your own toast on the range, loads more stuff. Also the original concrete cows have been moved to the grounds too.
It’s one of the greenest cities in the UK so there are loads of parks - the Parks Trust looks after lots of them as previously mentioned and there are usually lots of events through the year. The Tree Cathedral is a bit different and beautiful - lots of trees planted using the floor plan of Lincoln Cathedral - trees are now mature so it’s a beautiful space.
Xscape has a big multi cinema, indoor ski-ing, indoor ski diving, indoor bowling, indoor climbing, trampoline park and plenty of restaurants
There are other trampoline parks and inflatable ones too.
The robotazia restaurant should be fab (I’ve only been to the pop up one in the library which was really popular),
There was also a place with scaletrix type cars to race, a board game cafe, several indoor climbing places, pottery painting cafes, indoor or outdoor crazy golf,
There are at least two virtual reality places that most kids adore.
The theatre is great and has some great shows. There’s an interesting art gallery next door with a cafe that overlooks the main park and has great views over the countryside.
Check out the Milton Keynes Kids Facebook page for loads of free things to do around the area.
MK Mums site has paid-for places as well as free ones. They also do a year’s card that has lots of offers on - worth checking out to see if any of the places you want to go to are included as they do things like include an extra free hour or take a kid for free so might be worthwhile.
Destination MK website also has other ideas on.
Check out MK Play Association too - they run free play sessions all over MK through the holidays which might be fun.
Also MK is on a main railway line, so if you can get to Edinburgh or Glasgow you should be able to travel there directly (with just 1 or 2 pretty easy changes) without the need for going into London. Also check out the split ticketing option on money saving expert for easy ways to cut down ticket prices.
If your kids are football mad, MK Dons have their stadium built into a hotel (or maybe the other way round) which might appeal.
There’s more but I think this post is long enough - shout if you want more ideas or info.