The bigger boats can mean bigger prices and a big disappointment but if you read my review on Tequila Sunrise Charters from last April you can see how good "big boat" fishing can be. That trip was the most amazing fishing experience of my life. Multiple sailfish, mahi mahi and a tuna on a four-hour trip.
As you have indicated, fishing for bonefish down towards Punta Allen in the Sian Kaan can also be really fun. There is one outfit (Pesca Maya) that will pick you up from your resort, drive you down for a day of fishing and then take you back again. I did that about 6 years ago and caught quite a few bonefish. Not cheap though.
You can also charter a panga for 3-4 hours in PDC, PA or Akumal. I did that two years ago and hooked into a big sailfish that was lost right next to the boat. You just have to be careful to get someone who knows what they are doing. Way cheaper than the big boats...
That jigging for amberjack looks like fun - have to try it sometime.