The 2016 FBI hate crime statistics are out, and as in every year, anti-Jewish incidents dwarf all other anti-religious incidents - combined.
684 of the 1273 anti-religion incidents were against Jews.
Anti-Muslim incidents have gone up significantly in the past few years, though. 381 of the incidents were anti-Muslim. That number is more than double the 154 in 2014. (The antisemitic incident number in 2014 was 609.)
Breaking down the incidents further, anti-Muslim incidents tended to be much more violent than anti-Jewish incidents. 127 of the anti-Muslim incidents were assault (aggravated or simple), as opposed to 73 of the anti-Jewish incidents.
On the flip side, the antisemitic incidents were concentrated in destruction/damage/vandalism (489) and intimidation (238).
I read this to mean that Muslims are more likely to become the victims of sudden rage when someone sees a recognizably Muslim person in the street, while Jews are much more likely to be the victims of those who want to target the larger Jewish community by targeting synagogues and Jewish cemeteries.
The FBI doesn't look at the religion of the offender, only the race, so it is not clear how much of the anti-Jewish crime is done by Christians or Muslims or anyone else.
It is interesting that the relative uptick of anti-Muslim crimes follows the warnings of "Islamophobia" we were hearing about in years past when such crimes were far less prevalent. Cause and effect are not easy to distinguish, but it is almost like the warnings of Islamophobia are becoming a self-fulfilling prophecy.