A regular hole saw will get the job done. If there is any wood in the gunnels, take the time to go and get some marine epoxy from bunnings (it's 2 part and sets white) to seal any exposed surfaces before fitting the rod holders. Then make sure you seal the screw holes and around the rod holder with sikaflex 291. 

 make sure they are in the exact spot you want them . get yourself a decent hole saw and take your time drilling through. taking in mind if the holder is on an angle drill through on the same angle. and make sure there are no wires hidden under or are going to be in the way for the holder. when mounting the holder use a decent washer under the glass to avoid any pressure cracking the glass. hope this helps 

Hole saw works a treat through fibreglass. To stop the area around your hole cracking or chipping, cover the area in the blue painter’s masking tape and when the hole saw teeth hit the gelcoat put your drill in reverse and keep going so that you are ‘grinding’ away the gelcoat until you get through to the fibreglass and then put it back in forward to cut the hole and finish it off. Same technique with drilling holes for the screws.

 helps alot will give it a crack tommora 

 When i run a hole saw through plastic or fibre glass I start of in reverse so the teeth dont bight in too hard. This will strart the hole without cracking the surface or grabing and jumping around.

If the hole saw binds up on the fibre glass, rub a bit of candle wax on the saw , this will lubricate it as you cut. 

Also with rod holders on an angle, i usualy cut one into a thin bit of ply as a template ( Test ) as the hole is not round. 

 You gotto love this forum. Excellent advise above. The only thing I could add is that if you don't have the correct size you can go smaller and use a dremel rotating tool with a small round sanding wheel. These make very light work of sanding this stuff and I used this technique when cutting the hole for my seacock into the bilge. Just go slow and check constantly for size.