You should be able to recover your notes data from a Time Machine backup as follows:
- Enter Time Machine from the Time Machine menu
- Use the timeline (it's on the edge of the screen) to locate a version of the Notes storage folder from before your clean installation of macOS Sierra. (The location should be ~/Library/Containers/com.apple.Notes/Data/Library/Notes/ where the '~' indicates your user account home folder)
- Select the folder and click on Restore to restore it
If you haven't got a TM backup or want to try recovering the data from your HDD, see below.
Extracting notes data from your HDD
If you haven't got a TM backup or can't get it to restore from one, you can manually extract the data using a web browser (e.g. Safari, Etc).
To do this:
Go to the location on your HDD that is equivalent to the following path:
Inside this folder you'll see files with names such as NotesV6.storedata
Copy these files to another location on your SSD
Add a .html extension to each of them. (Note: You will be prompted as to whether you're sure you want to use the .html extension - click on the Use .html button).
Use Safari or another web browser to open the NotesV6.storedata.html file first (it may not be 'V6' in your case, but it will be 'V' followed by a number)
You should now see your missing notes
Now go through the process of copying and pasting the data into new notes and saving them
If any of your notes are missing after going through the above steps, repeat Step 5 and open the other files you copied across at step 3 to see if your missing notes are there.
Let me know if you run into problems.