For the overall organization of a cell:
* Cellular architecture
* Cellular organization
* Cell morphology (describes the shape and form)
* Cytoskeleton (refers to the internal framework)
* Organelle arrangement
For specific parts of a cell:
* Organelle (for a specific functional unit)
* Component (for a part of the cell)
* Structure (general term, but can be specific)
More general terms:
* Anatomy (for the structure of living things)
* Microanatomy (for the detailed structure of small things)
The best alternative will depend on the specific context of your writing.