Tokyo Kyoto: Hikari Tokkaido:
One-way fare: approx. 13,000 Yen
Kyoto Kanazawa: JR Thunderbird
One-way fare: approx. 6,700 Yen
You can save 1,680 yen, which may allow you to buy 2 to 5 box lunches, by purchasing a base fare ticket from Tokyo tokunai (within 23 city wards) through to Kanazawa; this ticket will be valid for 5 consecutive calendar days.
(You have to purchase an express ticket separately for each train ride, but as to a base fare you can combine legs of plural train rides, which might save money if they have no section in common.)
I am heading over to Japan in about 6 weeks for a university trip
That means it will be around
26 March 2012.
I recommend reserving your seats early because your ride may be taken during spring holidays.
Compared to Golden Week, O-bon days and New Year holidays, I guess it will be easier to reserve a seat; however as to Shinkansen, in case your time span allowed to take a train is small, you might have to use a non-reservation car if you don't try reservation until the last minute.
(You can change cars from a non-reservation car to a reserved-seat car in order to take a vacant seat by paying for the gap in charges, but not vice versa.)
JR companies will revise their diagrams on 17 March 2012.
Please be sure to use new timetables, which are expected to be available on the Web within a week or so.