I'll be in Puerto Rico in January, and four of us need to get from San Juan to Fajardo on a Monday morning. I know there are public buses, as well as shuttle buses, but I think there are also private cars that could take us. It seems like a private car might be the best option since 4 of us would fill it, making this cheaper than a shuttle, not to mention faster. But is this the best option? By best I mean: both cheapest and fastest, which I think it may be!
Personally, I'd definitely go for renting a car. Puerto Rico's a very car-centric place and you really need to your own wheels to get around anywhere outside San Juan (and arguably there as well if you plan on venturing outside the old city walls). Roads, signage and driving isn't too far behind mainland US standards, especially compared to what you see elsewhere in Central America and the Caribbean, so it's the easy option as well. Plus they even use kilometers and liters like sensible people... although for some bizarre reason speed limits are still in miles!
A taxi from San Juan to Fajardo would cost you around $80 one-way, which is pretty poor value compared to just renting a car for $50-ish/day.
I'm not sure what buses you're talking about, since as far as I know Puerto Rico's only long-distance public transport option is the público, which is really just a shared taxi without a fixed schedule. (San Juan does have scheduled buses, but they're all local services.) They leave from awkwardly located terminals at random times when they happen to fill up, and unless you get there at the hairy butt crack of dawn (6-7 AM), you may be in for a long wait. I made the mistake of showing up at Ponce's terminal at 10 AM once, and it took me two hours to get a ride to San Juan, this on what's probably the "busiest" route in the territory between its two biggest cities. Once they do get going, they stop randomly along the way and at your destination to drop off people, which also makes them far slower than driving from point A to point B by yourself. Pretty much the only upside is that they're cheap, SJ to Fajardo would be around $5/head.