Currently my site has a lot of 301 redirects we are managing in our .htaccess file (several hundreds 301 redirects); however, I am wondering would it be better and more optimal I use a plugin such as Redirection to accomplish this?
This is not really a clear question, and plugin suggestions are usually closed, as per the FAQ http://wordpress.stackexchange.com/faq
It all depends on what kind of work you want to do: either edit .htaccess or work with a plugin GUI.
Redirection works well and will allow entry of rules via CSV file and logging of all redirects as well as 404's.
With Redirection, you sacrifice a amount of site performance, but it may be worth it to you.