4 hour transit in Haneda Airport

Will be arriving in Haneda Airport via JAL on a Sunday morning and departing on a domestic flight(also JAL) 4 hours later.

Need advise on things to do during the transit layover. Will be purchasing Hokkaido Rail Pass at JR EAST Travel Service Center as well. Possible to travel to and fro to Tsukiji Market?

Can i check in to domestic airline immediately once I arrive in Haneda?

Domstic flight check-in limit is 15 min before.
But no exact yr flight arrived on time or serious delay(even cancel) happened.

Re book later flight or stay one night in Tokyo area if rally want to go Tsukiji.
http://www.japan-guide.com/forum/quereadisplay.html?0+153736

Leaving the airport and coming back with just 4-hour layover is not recommended. At least 6-7 hour overlay would be better. This is esp true if it's your first time and you're wasting time trying to find the right platform, the right exit, how to buy fare at the machine, navigating on foot from station to market, etc. Also if you hop on the wrong train and need to hop off to correct your route. All of these will eat away at your time.

If it were me I would head for the World Trade Center. There's a nice observation deck directly above the monorail platform, so no need to navigate any streets and no risk of getting lost. Cup of coffee, enjoy the view for a bit, then back on the monorail.

Have to say you would be brave to leave the airport. I personally would because I couldn't sit around for that long, but it's a risk. At the very least if you are dying to go into the city, the above is a whole lot safer than the market (which is best enjoyed when you're not rushing around like crazy).

And I actually think that there is a very good chance you could make it to the market and back in time. The question is whether or not it is worth the risk for such a short visit to the market. In my opinion: absolutely not!

If you're arriving on an international flight, don't forget the time it will take to go through customs and immigration either. The couple times I've flown in internationally to Haneda the lines were benign, but that is something outside of your control.

I think going to Tsukiji would be nuts, but the WTC suggestion is a good one.

Thanks all for the suggestions. We been to Tsukiji twice before by train so should be ok for us. On 2nd thoughts, it's really too rush thinking back.. :)
World Trade Center (2 Chome-4-1 Hamamatsuchō
Minato-ku, Tōkyō-to 105-0013) is above Hamamatsucho Station ?

According to Google Map, it take around 20 mins. So there is to drink coffee and relax huh?

Yes, when you arrive on the monorail you can see the building the WTC is located in right above the terminal. The rapid service is around 20 minutes, and there are express and local services which are a bit shorter/longer.

Allowing for a ~1 hour round trip to Hamamatsuchou, there is definitely enough time to do this without feeling particularly rushed. But I will say that if it happens that your flight arrives late then you should use very good judgement on what to do. The suggestion really is based on the assumption that everything will be running on time.