Unfortunately, these situations can be very difficult to diagnose without a ton of details. I will say this, though, and I know it's a hard thing for many people to hear. Negative SEO is very rarely effective unless there's already an underlying problem. It may not be a deliberate ("blackhat" SEO) kind of thing, but for a negative SEO attempt to succeed it could mean that:
(1) There were issues with your link profile you are unaware of. This could even be a handful of links that violate a specific guideline and that are easy to overlook. Remember, it's about Google's perception of quality, not yours (and their perception wins).
(2) There's some technical issue (say a crawl issue or large-scale duplicate content) that's make you more vulnerable.
(3) There's a content quality issue on some part of the site that's harming the rest of the site.
Dig deep, because it's easy to see some errant 3rd-party links and assume that's the entire problem but in 95%+ of cases, it isn't.
If it's really 100% bad links from someone else, disavowing and requesting reconsideration are about your only option, Unfortunately, if it's Penguin, then you have to wait for an update in most cases, and we're many months since the last one. In most cases, though, it's a combination of factors, and you may have control over some of them.