If buy from Shinjuku, is more ex bcos it includes the Romance train ride from Shinjuku to Hakone Yumoto.
However, if you got JR pass, take Shinkansen to Odawara then buy the Hakone Free Pass there, cheaper.
Hopefully, your luggage is not too big, the mid and large sized lockers not so many (click on 7, 21, 30, 31). Else, there is a Hakone Baggage Service (click on 8) and Baggage storage desk (click on 10).
If you're just doing the loop and don't deviate to other attractions in the same area, <5-6 hrs including lunch should be sufficient.