The simplest way is to override the Bootstrap styles with your own CSS (your option #4). Your CSS styles can be defined in a separate CSS file or <style></style>
markup that follows the bootstrap.css in your HTML...
.thumbnails {
border:0;
}
Another way is to generate a custom build of the Bootstrap CSS (your option #1) using the http://twitter.github.io/bootstrap/customize.html tool. The downside of this is generator limitations and maintaining your own custom build.
Finally, there is LESS, a dynamic style sheet language that is compiled to CSS. LESS supports the ability to nest selectors and to create variables. You'll find a more extensive thread on LESS here: Twitter Bootstrap Customization Best Practices.
If file size or performance is a concern checkout BootstrapCDN http://www.bootstrapcdn.com which serves the combined Bootstrap minimized from a CDN. The CDN serves up Bootstrap at Bootply which is a tool I built to test, prototype and customize Bootstrap.
Good luck!