They could stay where they are for a little longer or you could up-pot now. Tomatoes benefit from up -potting, when you bury them deeper as imafan said.
This year someone gifted me with a bunch of plastic pots that are 2.5" square at the bottom, 3.5 in square at the top and 5" deep. Great for tomato seedlings to let them grow long roots. But I'm having trouble finding them to order more.
Otherwise, I don't know if you have them in Belgium, but here they sell these 16 oz plastic cups (Solo brand) cheap in packs of 50 and they work great for tomato seedlings:
But up-potted or not, your seedlings will not do well on the window sill for much longer. Not enough light, they will start stretching. It will take a week or so to get them hardened off. If your weather is on a warming trend, you can start now, just putting them out for 1-2 hrs the first day and increasing daily.