When comparing vimwiki plugin for vim vs Gingko, the Slant community recommends Gingko for most people. In the question“What is the best cross-platform note-taking app?” Gingko is ranked 21st while vimwiki plugin for vim is ranked 23rd.
Specs
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Pros
Pro Internal link makes it easy to create a knowledge network
Pro Comfortable for Vim users
Has a very minimal learning curve for people already used to Vim, as the preset shortcuts are very easy to learn and don't conflict badly with other Vim behaviors.
Pro You can customize colors
Pro Allows focusing on one piece of information at a time
Since Gingko documents are "trees", they are always organized on the go. And since everything is written in cards, it is possible to focus on one chunk of content at a time.
Pro Easy to overview
Despite the complexity of the tree structure, it's always clear where you are, and how to quickly add your thoughts.
Pro Markdown support
All formatting is done via Markdown.
Pro Non-linear
Non-linear notetaking allows you more flexibility, freedom and creativity.
Cons
Con Limited to use with vim only
vimwiki is a plugin for vim, so you won't be able to make use of it if you're not a vim user (and don't want to be).
Con Limited free version
The free version is limited to 100 cards and 10 documents. Depending on how you use it, this might not be enough.