San Ignacio is my favorite place in Belize. You're close to caving, hiking, ruins and all that sort of stuff. You can walk around and be perfectly fine. Belize City is the pits, though. I wasn't impressed with the beaches, either, though the snorkeling near Ambergris Caye, Belize is worth doing.

You can take this trip from Lago de Atitlan.  Monumento Natural Semuc Champey is one of the best places I have been in my life. They are natural rock pools in the middle of the jungle.  there is also a cave tour where you swim with candles in your mouth.  then cruise down the river in tubes afterwards.This place rocks. If you're in the area, its a must.

Unless you have the budget to make small flights at a high cost, I would chose one or the other. Also Belize can be a little ruff if again you don't have a budget for private transfers and resort style hotels. Basically you pay not to see the real Belizebut if you have the cash there are beautiful ruins and coral reefs.

Guatemala doesn't have the beaches but Flores is great and the  and the gateway to Tikal!  

If you want a little spelunking adventure, do the ATM Tour by San Ignacio in Belize! I just came back last week and it was an amazing highlight.

I would definitely recommend Lago de Atitlan in Guatemala. You can travel to each little town by boat on the lake, make sure you go to San Marcos La Laguna. Atitlan is a beautiful place, and you can even take a guided tour to one of the semi active volcanos. Tikal is also amazing, But that is a little out of the way and needs to be an overnight trip if you have the time!

I'd definitely recommend both Tikal and CaracolCaracol; stunning remnants of the Mayan civilization. If you have a short amount of time, can choose one or the other.

In Belize, seeing the reef around Ambergris Caye, Belize is definitely a must, particularly if you like snorkeling/diving.

The highlight of Guatemala in my opinion is Antigua Guatemala (a great place to spend a few days), followed by Lago de Atitlan.  

Lago de Atitlan 

Visit Lago de Atitlann in Guatemala! There are several little towns around the island, and you can get around easily by water taxi.  There is kayaking in the lake, beautiful Eco-lodges to stay in, and if you're feeling up for a workout you can hike Volcán San Pedro, which gives you amazing views! Hardest hike I've ever done (10k feet straight up), but worth it! 

Being down the chain of this question let me mention cool places others haven't so far:

Guatemala

1. Mayan archaeological site Yaxhá in Petén province. I personally liked it more than Tikal since you can barely see any tourists there, it is very well preserved and you can actually climb to the top of the most pyramids there. >>SEE GALLERY<<
   
   
2. Monterrico - a nice coastal retreat on a Pacific side of Guatemala. Ocean is a bit rough, more for a surfing, but what was really cool was Mangrove Natural Reserve tour and being able to see sea turtle hatch eggs at night on the beach. >>SEE GALLERY<<
   
   
3. Chichicastenango - is well known for its famous market days on Thursdays and Sundays where indigenous vendors sell handicrafts. >>SEE GALLERY<<
   
   
4. Biotopo del Quetzal near Cobán where you can hike in tropical cloud forest and if lucky to see resplendid bird quetzal (I did see it!)
   >>SEE GALLERY<<
   
   

Belize

1. Actun Tunichil Muknal - also known as ATM, is a cave near San Ignacio known as a Mayan archaeological site that includes skeletons, ceramics, and stoneware. One of the coolest things I did in my life when it comes to caves. It's deep in jungle and you will have to wade sometimes in the cave through water up to your neck.
   >>SEE GALLERY<<
   
   
2. Cockscomb Wildlife Sanctuary near Dangriga. Even though Dangriga itself is an ugly town where there is nothing to do, hiking in sanctuary gives you an opportunity to see some animals. I was lucky to see peccari (skunk pig), fresh footprint of jaguar and passed just a few feet from one of the most venomous snake Fer-de-Lance.
   >>SEE GALLERY<<