Hi Clernix
Here are my thoughts for your trip. If you want three goliath boat trips, my recommendations as to dive sites are:
1. Zion Train wreck trek (90') coupled with a wreck called MG-111 (60') both off of Jupiter. These can be done on a single 2 tank trip. Ask the operators about this. I prefer to use an operator going out of Jupiter Inlet as it is closer to the dive sites. Operators from Palm Beach may, or may not, go to these sites, which are far from Palm Beach Inlet so why take chances? As for operators, either Capt Sl8r, or Jupiter Dive Center. Both are excellent.
2. Mizpah, as Danvolker mentioned, a really great wreck. BUT, it is close to the inlet so you want to do this on a HIGH TIDE if at all possible, otherwise murky water from the bay might lower the vis. Yes, this does make a big difference. Check tide tables to see if you want a morning or afternoon trip based on the tide. For this, use an operator going out of Palm Beach Inlet: My favorites are Jim Abernethy, Narcosis Dive Boats, Pura Vida Divers.
3. The Castor wreck off of Boynton Beach. Of the Goliath spots, I think this one is the very best, and the wreck is fantastic. You need to use an operator out of Boynton Marina. I like Splashdown Divers or Underwater Explorers.
I would not allow multi-trip discounts to persuade you to concentrate on one operator. The Goliath aggregation is fantastic and since this is a special trip, I would hit all three of the spots, even though you may have to use different operators for each.
You don't have to move hotels to do these different dives, all of these are within a 30 minute drive of any place you might stay in the Palm Beach or Jupiter area.
As for where to stay, you have a lot of choice. My first recommendation would be that Best Western in Jupiter. It is walking distance (across the street) to some great restaurants and a great dive shop (Scubaworks) if you need any gear, and 5 minutes from either Jupiter Dive Center or Capt Sl8r. It is also 5 minutes to a really nice beach right at Jupiter Inlet. The hotel itself is very decent and is on a walkway that takes you about a mile along the intracoastal to a primitive preserve with trails, if you like a little exercise. Allow about 15-20 mins to Blue Heron Bridge and the Palm Beach boats for the Mizpah. Allow 30-40 mins to drive to Boynton for your Castor dive. If you want, do the Castor the day you check out and you are already on the way to the Keys.
Near north Palm Beach, there is nothing for accommodations under $100 that is quite as good and also so close to really nice things to do. That is no big deal as everything nice is a pretty short drive away. The motel 6 on Palm Beach Lakes seems to have fans. At Blue Heron blvd and I-95 there is a Red Roof In and some other cheap hotels. I have stayed there and they are fine, but nothing to do at the hotel proper and you don't want to walk around the area. But, you can save some $ over the Best Western if that is important.