At the airport there are several transportation agencies, they can offer you a private chauffered vehicle, a little bit more expensive than a taxi. This will be perfectly safe.
Here are a few options for a day visit:
Malecon 2000 and Cerro Santa Ana (there are several museums near the Malecon)
El Morro (dolphin watching)
Malecon del Salado (water fountains, can be combined with Malecon 2000)
Bosque protector Cerro Blanco (Tropical rainforest)
All these places are perfectly safe.
I would not recommend going out at night on your own. There are several clubs and nice places to hang out (unfortunately they are seasonal and go by fashion, meaning the same club I was 3 months ago may have changed names and is no longer at the same place) it is in like any big city you choose the wrong place and .... . Unfortunately I do not know of any companies offering a good pub crawl in Guayaquil. On the other hand if you want to go out for Dinner, there are several amazing places to eat (they can get you a trusted taxi cab that is safe for your return to your hotel):
La Parillada del Nato (steakhouse)
El Caracol Azul (seafood)
Resaca (seafood and other, also some partying available. Safe)
Mannys (Best crabs in Guayaquil, ok - this is disputable, let me rephrase: best crabs in a safe neighborhood in Guayaquil - Id love to recommend hidden finds but you may not find them and not safe going on your own)
Voyagers Travel Company