I am a data engineer earning $110,000 (currently that is 99000 Euro) paying for my own health insurance in San Francisco. I have an offer from a startup in Netherlands for a similar position at 52000 euros + 8% of gross income as one time yearly payment and a $1000 moving allowance. I feel there is not enough data on Glassdoor or other sites for me to make a judgment on the average salary in Netherlands. Since the responsibility is similar in both jobs, is this salary a fair pay?
Firstly, Amsterdam is a fantastic city and the Netherlands is a great place to live. :-)
EUR 52k per year gross is around EUR 2900 per month net. That's a decent salary in the Netherlands and somewhat above the average, but accommodation in Amsterdam is expensive. To give you some idea of costs - if you're renting a place on your own, you won't find much below EUR 1000 per month, but you can get cheaper sharing with other people (others can probably give more info on this). Health insurance is mandatory and costs around EUR 90-100 per month - everyone pays the same, regardless of age, pre-existing conditions, etc. It's likely that you won't need a car. Buy a bike and get around more or less for free (careful of the canals), or use the good and comprehensive public transport.
You should also check out the 30% rule which allows foreigners taking skilled work to get 30% of their salary tax free in some circumstances. Your employer should know about this. It would be worth around EUR 600 per month extra to you. Also check whether your employer covers pension costs.
I can't compare with what you have now in San Francisco, but you can live well in the Netherlands for this kind of salary. Edit: you could try negotiating a little more for relocation costs. USD 1000 is not very much given your circumstances.
I'm not sure about the level of life in SF but I heard that housing, medicine and child care is quite expensive.
As for me, DS is a quite hot area and I would expect more high salaries than 56k.
And 1000$ is not enough even for the ticket from SF to AMS.
Keep in mind also that US citizen might have to pay double taxes in NL.