Publishing tables in a paper
Where you include the tables is entirely dependent upon how important the information within the tables is for the text.

Three pages of tables are a lot. An average paper is somewhere between 5 and 20 pages, so three pages of pure table in between the rest certainly disrupts the text, which speaks against option (1). Option (2) will force the reader to go to the appendix, depending on how important it is that they actually read the table. If you could extract the key information in text form, you could simply reference the large table and put it into the appendix. Supplementary data is more likely to be overlooked by people reading your article, as they are separate documents that can be found on the journal web page. Therefore, I would only choose option (3) if the actual values in the table are unimportant and the statistics can be extracted in form of text or a smaller table.

You say there are two additional tables that are important for your model. It sounds like these are a case for the appendix. Again, depending on the importance of actual values, they also might better fit into the supplementary data.