Transportation from CUN to Punta Allen
 

I'll be traveling to Punta Allen for a week in February. What is the best way to get there from CUN? I've heard the road south of Tulum is quite bumpy, and have also heard there is boat transportation. Have not found much on the websites I've looked at.

Cancún to Pta. Allen is first via the Cancún - Chetumal Highway, until you get to Tulúm, then "highway" 109. Total is 150 km / 93 miles. The bit past Tulúm begins to get narrower and you end up on sandy rutted and bumpy road past Boca Pailá to Sian Kaan Biosphere Reserve and ending in Punta Allen. See here and here for the road and alternatives.

A rented Jeep (or any high clearance) type vehicle is probably best, using Mexican rules - fill up at Cancún, again at Tulúm and again when you can; give yourself plenty of time - four to five hours gives you chances to look things over and stop, perhaps even replace a tire (be sure the car rental agency provides you a good, serviceable spare, tools, etc.) Some experience at driving this type of road helps.

We had a great trip. It took about 2.5 hours from Tulum to Punta Allen. Very bumpy and slow going, and lovely. Well worth the trip. We hired a van and driver. On return trip, the van broke down (one too many bumps!) and luckily we were just outside of Tulum. They sent a replacement van within 30 minutes. Very well done.
I can't recall the name of the company but will post it when I can locate it.

I did it in a smallish rental car, stayed overnight.

No problem, just take your time.
There are "ecotours" of course, for a price.