Here are some alternatives depending on the situation:
For general thinking:
* Contemplating - implies deeper thought
* Cogitating - a more formal way of saying thinking
* Reflecting - focusing on past experiences
* Considering - weighing options
* Mulling over - thinking about something casually
* Pondering - contemplating something seriously
* Reasoning - using logic
* Imagining - creating ideas in your mind
* Daydreaming - letting your mind wander
For specific types of thinking:
* Deciding - making a choice
* Analyzing - breaking down information
* Solving - finding a solution
* Remembering - recalling information
* Learning - gaining knowledge
* Understanding - grasping the meaning
* Planning - creating a course of action
For more informal situations:
* Figuring out - trying to understand
* Working out - thinking through a problem
* Coming up with - generating ideas
It's important to choose the word that best reflects the specific type of thinking you want to convey.