How long to clear customs at Narita?

I was wondering how long it should take to clear customs at 3 pm arrival as my schedule need to grab a bus at shinjuku on 6.30pm.

It typically takes about 30 minutes (not busy) to one hour (busy) from landing to clearing customs.

The fastest way of travel from Narita Airport to Shinjuku is by Skyliner and Yamanote Line via Nippori . It is usually 20 minutes faster than taking a direct NEX.

In order to catch a 18:30 bus, you should be taking the 16:38 Skyliner or 16:19 Narita Express (a couple minutes later if you board at Terminal 2).

I think your chances are good to catch at least the 16:38 Skyliner if your plane is not delayed and immigration is not overly crowded.

The downside of the trip by Skyliner is that on regular weekdays, the Yamanote Line is rather crowded and uncomfortable to use with large luggage at that time of the day.

Thank you very much.I plan to sent my luggage to my destination by takuhai-bin and travel lightly.So yamanote line would not a problem for me.It's about time that I worry.

Well, you effectively have 3.5 hours to reach Shinjuku. If you have no flight delays you can make it.
One hour for immigration and luggage. Half an hour to an hour to queue if you are getting some form of rail pass.
An hour to train to Tokyo from the airport.
Getting from Tokyo to Shinjuku the rest of the time.