Howellpix,
Where you want to stay is going to depend on what you really want to do on your trip.
If you want to go about and see sights in Hyde Park and other areas I think the B&B's would be a better bet for you. This will allow you to eat at a number of different restaurants that are in the area and are very nice. Make reservations for the Culinary Institute (sometimes it is difficult to get in). Traveling six hours to get into the Hudson Valley is well worth it and you will enjoy your trip. The B&B's are the way to go if you are going to be out and about and traveling throughout your visit.
Mohonk is a much different experience. Mohonk is a trip within itself. It is basically almost a cruise on land. You must understand that Mohonk was started in 1869 and except for the new spa has not had any major construction since about 1910. The building is very old and the walls are thin. You will hear things that you might not think you would in a regular hotel room. The rooms can be small, but then again you shouldn't spend too much time in your room. There are no TV's in the rooms and only a few have radios. There are some public tv viewing areas. Mohonk is a wonderful place but you must be willing to leave behind some of your 21st century thinking to enjoy it.
If you are going in late March some of the trails will be closed. Most of the carriage paths and better known trails will be open, but not all. You won't want to leave the House once you are there. It is about a 20 minute drive into New Paltz and use your time there to just relax and renew your mind body spirit and soul. Really it all depends on your personal taste. I love Mohonk and could spend an eternity there, but Mohonk is a place you love or you hate. Not many people seem to come away and say "oh it was alright, I guess I could go back." You are either always going to want to go back or never go again.
If I were you split your trip up. Do two or three nights at Mohonk and then book the rest at the B&B. This will give you the opportunity to experience both. Relax a bit in the mountains and then for the latter part of your trip you can do some exploring or vice versa.
I hope this may help you in your decision. If you want more just ask. I know Mohonk very well and am more than happy to talk about it. As far as the B&B's go, not as familiar with them, but I do know the area very well.