Just a little quibble here: I think you are referring to New Amsterdam, before it became New York. Yes, that was the first place in what is now the United States where Jews settled in 1654. They were Sephardic Jews (i.e., of Spanish origin or descent) who arrived from Brazil.
BTW, I was unaware that Lutherans and Catholics were not allowed to build churches there at the time. I believe that the Dutch were considered the most socially and economically advanced culture in Europe then, so it's a little surprising to me.
The Dutch agreed to let the Jews stay in New Amsterdam after some initial objections, but that's not the same as allowing a synagogue to be built (and of course, it would have taken some time for the community to be able to afford to build one). I would need to do some research to find out exactly when the first synagogue was built and whether it was under Dutch rule or under early British rule when most of the people in charge were still Dutch but the British had final authority. I don't want to run the risk of giving wrong information based on memory.
On the broader issue — yes, the Dutch of the 1600s were very tolerant toward Jews, but not toward most other religious groups. I think it can fairly be said that the level of toleration extended by the Dutch to Jews was truly unique, was of a very different character from how many other dissenting Christian groups were treated, and was based largely on the sort of theology that develops in a church which places a very high value on the Hebrew Bible rather than just the New Testament.
For example, the international Synod of Dordt (sometimes spelled “Dort”) was held specifically to expel non-Calvinists from the Dutch churches, and the canons created by that synod found wide acceptance elsewhere in other Calvinist churches of Europe. The Dutch were nothing if not precise in their theology.
The Dutch government and the de facto “state church” had a wide variety of different attitudes toward other churches, ranging from full fellowship with some churches that shared the same faith but a different language and ecclesiastical structure, on the one hand, to open hostility with regard to some church groups such as the Remonstrants. The Dutch attitude toward Roman Catholics was the most severe of all, which is not hard to understand considering that the Dutch had only recently been ruled by Spaniards who had killed thousands of Protestants and tried to impose the full vigor of the Spanish Inquisition in the Netherlands. As a Jewish person, you know far too well what that meant for Jews, and Protestants weren't treated very well, either, by the Spanish rulers sent to re-Catholicize the Netherlands.
Full equality for Jewish people is now pretty much an accepted principle of American politics. There was a day when that principle was radical and had to be defended.
For those of us who are conservatives and value original intent of the Constitution, we need to affirm that the clear and obvious original intent of the Founding Fathers was to extend full rights of citizenship to Jewish people and to Roman Catholics. That was not the case in England, it was not the case in most Protestant countries of Europe, and it was a truly radical position for its time.
We need to affirm that position if we are going to be Americans who value the Constitution. The Constitution is not a “wax nose,” words have meanings, and we can't use liberal methods of interpretation to twist the Founders’ words in ways they would never have recognized.