There have been a number of high profile twitter account hacks and it's quite likely it's not always down to twitter.

You may use third part software to access and post to your twitter account, mainly because of the convenience. However, each time you allow a third party to gain access to your account you're opening another door for potential attack.
You passwords and the security for the third party software has to be at least as good as your two-factor authentication, however, it's unlikely.

If a determined hacked decides to look at your social media tools they could decide to try and hack those, rather than to attack twitter.

One of the first things to do is to disable any unused third party tools as soon as possible.

Secondly, make sure you use an unrelated, and strong password on the third party service. Of course, that won't guarantee complete protection, but it's possible that the third party applications could be the weaker link.

Log into your twitter account and and check your settings and applications that have access to your twitter account. Remove any that you no longer use. You can always re-enable them later.