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Lago Attitlan is super touristy, and there are a bunch of ladrones around the trails... San Marcos and north of it is OK (relatively safe) though.
Best hiking in Guatemala is in the mountains to the east of Chichicastenango. Not many people go there, small villages without roads here and there and very friendly locals.
About the jungle, depends If you go in wet or dry season. If you never been in the jungle, go with a guide. There are nice tours to hidden ruins and stuff. Wouldn't recommend to try by yourself of you have no experience with the terrain, it's tricky.
A nice trip is also in Antigua, hiking up the mountain next to the active volcano, from there you can actually look down into the crater. Eruptions are frequent, so bring a camera and tripod. Tons of companies offer guided tours for this, but you can easily do it by yourself. Spend the night up there while your at it...
I can tell you tons more if you want, spent about 2 years up and down central America.
