What is the best way to check mileage of bike?

Well, sadly enough, there does not seem to be any other truly scientific method available for the purpose. The standard method is what you stated on your question.
I would suggest you to fill exactly one litre of petrol when it goes into reserve and ride the bike till you get back to reserve. That could give you a more accurate reading than when you fill the tank and check when it comes to reserve.

Mileage is a great issue for middle grade people in India and I hooked up some mechanics and found some techniques to find Mileage.

1. First method you yourself told in question, so I don't want to repeat that here.

2. This method works best
(i.) Move to the Any Alignment shop, they have alignment machine. Put back tyre of your bike on the machine and accelerate. From this you will find Highway Mileage because you are actually accelerating your bike without applying much brakes; Now note the reading.

(ii.) Do same as before but this time use a mixture of clutch and brakes while accelerating. This will give you an estimate of average Mileage in the city area.

If you find that your Bike Mileage is poor then you can changing Engine Oil or driving Bike at Economy.