Then I wouldn’t expect any substantial delay because of perceived ethnic/religious identity at US airports of entry. Maybe a somewhat increased chance of being sent to Ag inspection, but most probably nothing more than that (if even that).
LAX routinely sends everyone (American and Canadian Citizens included) on Asian Flights (or at least PVG) to Agriculture Inspection. It usually isn't much more than an X-Ray, but it can take an hour or two.
At LAX, maybe, and with all the Asian flights and what people put in checked luggage coming from Asia, that taking a long time there doesn’t need surprise me. But the OP was asking about perceived Muslim identity. Given how often my travel party members — which does include Muslims and/or those with Muslim-sounding names — and I go through (or assume some or all of us may go through) Ag inspections at US airports of entry in the CST and EST time zones, it’s almost never been because of perceived religion of my travel party members; and I can’t recall the last time Ag took us more than 30-45 minutes at any of these US airports in the NE/MidAtlantic and Midwest. There are times when almost the whole flights seem to be sent to Ag, but that was based on route/flight rather than any explicit selection based on perceived religious affiliation. Our coming in on European or US carriers via Europe seems to mostly spare us this.
My suggestion for perceived Muslim foreigners flying into the US is that JFK, ORD and MSP are amongst the better US ports of entry to reduce the chances of being hassled on the basis of perceived religion.
My apologies for any confusion. I was commenting on your comment and the fact that OP would be flying from TYO: Maybe a somewhat increased chance of being sent to Ag inspection