Edinburgh is my favourite, but all your options sound good.
Edinburgh is walkable but also has a superb bus service that is widely used by visitors and residents alike. Just remember to thank the driver as is customary on getting off!
Dynamic Earth next to Holyroodhouse and the Scottish Parliament was a huge favourite with my kids - kind of interactive science museum where you ‘ go back in time’ in lift to start of the universe and then go through galleries over the ages to the present day through earthquake, tundra, iceberg etc. Incudes ride, 3D filmshow, rainforest and another film show at end.
The free Museum of Scotland has a good science hall with a racing car, hot air balloon and Dolly the Sheep, the first cloned animal. Inspired my niece to study bioscience! It’s opposite Greyfriars Churchyard ( many gravestone names are to be found in Harry Potter) and of course you must rub the statue of little Greyfriars Bobby’s nose outside.
Camera Obscura near the castle is great fun too. Great optical illusions and enjoy ‘shaking’ the tourists you see through the camera.
In the old town you can do a Witchery or other history tour telling you about the bodysnatchers for medical dissections, Deacon Brodie etc. Also see the site of the last witch burning outside magnificent St Giles Cathedral. Walk down to princes street through the gardens or via lovely cobbled twisty Cockburn street with its nice cafes, shops and gelateria.
Back down on Princes Street, climb up the inside of the Scott monument ( you’ll get your steps in) and recover in the cafe at very top of John Lewis in the new St James Quarter shopping centre. Fabulous views. Then visit the Lego shop or food court.
And, if after all that, you’re bored, hop on a fifty minute train to Glasgow and go to its science museum or transport museum.