Formal:
* Doubt
* Misgiving
* Distrust
* Skepticism
* Apprehension
* Uncertainty
Informal:
* Hunch
* Gut feeling
* Inkling
* Wary
* Leery
* On the fence
More specific:
* Accusation (when suspicion is strong and directed at someone)
* Conjecture (when suspicion is based on little evidence)
* Guilt (when suspicion is internal and focused on oneself)
The best synonym to use will depend on the specific situation and the level of formality you want to achieve.