Hello,
It depends on the usage. Custom tables are good for storing large amounts of data with a small growth of the database. Document types are used for documents, and every document takes more space than one line in a custom table. However, documents can be easily displayed in the content tree, there can be permissions applied...
You can create a document type, which will be the template of your documents and create those programmatically. You can find an API example by following
this link.
If you want to use it later, to be managable by the system, then I think the best choice would be the new document type.
Best regards,
Boris Pocatko