If you need to deal with the digital products/services both are good.
If you are foreigner and have no Estonia e-residency there is not much difference in the process of opening the company, public records, UBO reporting etc - both are in the EU so the legislation is pretty much the same...
If you do IT projects - Netherlands have very good tax opportunities. Both of these countries are strict in terms of opening bank accounts for non-residents, but I would say Netherlands have more option for classical banks.