Seems like HIS still has the best rates.
Honestly speaking if the price difference is not big i'd always get my JR passes from a local agent.
1) You never know the website agent may be from Russia or Africa (A friend once bought Eurail tickets online and never received it, email no reply, reported this but case/police cannot do anything cos not SG company)
2) Exchange rate/transaction loss
3) Courier fees if you do not buy a lot
4) No matter how slim, there is still a chance of "lost in mail"
5) If I have any problems, I can still go to my agent to have it solved
Just sharing my 2 cents as a regular Japan traveller