My neighbors went to Cancun in the off season last summer, and took 3 kids (youngest had just turned 5). They booked through Priceline and went to an all inclusive resort which was incredibly bargain-priced - I think it was $3200 for 5 people for a full week. In May and perhaps in April, it will be "off season" for you too so prices will drop. They had a pool and access to the ocean, lots of activities. They also rented a car and went off on their own to see things and go to other beaches, and they also did a trip to the ruins (which are beyond your children's interest at this point). Several of them scuba dive, but the 5 year old wasn't yet even snorkel-proficient. And they have a pool at home so kids are pretty water-savvy. So they just split up and did things separately. You could do this if you take your brother, but since your children don't know him well, you and your husband will be splitting up and taking turns with your brother.
I don't know if you can get your 6 year old snorkel-ready at home but I'd recommend it, as others have suggested. The 2 year old needs shallow water or a kiddie pool. If you rent a house, be extremely diligent about making sure the pool is completely fenced - I don't know what the laws are in other countries about child-proofing a house. You can fend for yourselves but you'll need to be very savvy about groceries and purchases, including water. Of course, the advantage is also that you can have kids napping or in bed at night and still be able to use the pool or sit outside. The Mayan Riviera area is generally considered safe.
Cruises are usually all-inclusive but as someone else said, your little one may be way too young for most of this. Kids need to separate easily from parents, and if you need to put a toddler down for a nap, that means one of you is in the room unless you hire an off-duty staff person as a sitter, and that would be extra. I think your brother may not have any idea how extensive these cruise line activities are for 30-somethings. But if he's decided, then he's decided.
Are you a member of AAA? They have a great travel agency, free to members, and they have a lot of promotions as well as a good rating system for hotels in all price ranges. But a lot of people book things themselves using Kayak, Priceline, Hotwire, etc. I don't think they book houses though.