While there are some caveats and complications to this answer, I would argue that Arabs and Muslims are, without a doubt, more marginalized in American society than Jews are. This is not to say that Jews are completely in the mainstream, but, particularly in post-9/11 America, Jews are much less marginalized than Arabs or Muslims.
Before answering, I must say that I live in the rural West where Jews and Judaism are not very visible. I therefore may be underestimating the degree to which they are marginalized. I did go to college in Chicago, where Jews are much more numerous, but I may have been too young (as well as too unfamiliar with ways in which Jews might be marginalized) to understand. These facts may color my answer.
I should also stress that it is possible for individual Jews to be more marginalized than individual Muslims and Arabs. For example, an Orthodox Jew who dresses and wears his hair in a distinctive way may be much more marginalized than an Arab Muslim who has assimilated and who looks like a “regular,” if somewhat “ethnic” American. Thus, we cannot make blanket statements about the relative degree of marginalization of all Arabs/Muslims and all Jews.
Overall, though, I would argue that Jews are much less marginalized than Arabs and Muslims. This was always true, but has become much truer since 9/11. The main reason for this is that Muslims and Arabs are now seen not just as outsiders, but as dangerous outsiders. People feel that Islam is at war with America. They worry that President Obama is secretly Muslim and is trying to impose Islam on America. (Of course, it is only some people who feel this way, but the point still holds.) There are no such worries about Jews in mainstream American society today. It is hard to conceive of mass protests arising if Jews were to try to build a synagogue somewhere. By contrast, there have been many instances of protests about mosques, even leaving aside the mosque that was proposed in Manhattan, not far from the site of the World Trade Center.
On the whole, Jews are seen as a “normal,” part of American society, even if they may be something of outsiders. By contrast, Muslims and Arabs are seen as a major potential threat and as people whose values may be completely at odds with American values. Therefore, I would argue that Arabs and Muslims are much more marginalized than Jews in the US today