With regards to security and convenience which cookies are better the PHP ones or the Javascript ones?
They are the same ones, in both cases the cookie is sent to the browser, stored there and the browser send it back to you every request until it expires or is deleted.
For that reason, you should never use cookie for security as your question implies nor for any data which you consider important to keep unaltered by the end user.
There are five things to always remember when you use cookie:
1 - you can not trust its content
2 - you can not assume it will still be there on the next request
3 - you can not trust its content
4 - you can not assume the user never visited before if it's not there
5 - you can not trust its content
If you get that, accessing cookie from php or javascript is simply a question of what's more convenient to you.