V1-V5 are different (sub) regions of the visual cortex itself.
The layers L1-L5 (some regions have a layer 6) refer to the different cellular strata in the depth dimension of the cortical mass. This stratification occurs to some extent or another in various areas. Different sections of the cortex, e.g., the primary motor cortex have a predominant level 5 (for the pyramidal tract). Something like the visual cortex has more cells in layers 4 and 6.
Layers 2 and 3 tend to carry interconnections between different areas of the cortex, and the topmost layer is generally less dense.