Это зависит от потребностей вашего проекта.
Преимущества проверки в каталоге Pods
After cloning the repo, the project can immediately build and run, even without having CocoaPods installed on the machine. There is no need to run pod install, and no Internet connection is necessary.
The Pod artifacts (code/libraries) are always available, even if the source of a Pod (e.g. GitHub) were to go down.
The Pod artifacts are guaranteed to be identical to those in the original installation after cloning the repo.
Преимущества игнорирования каталога Pods
The source control repo will be smaller and take up less space.
As long as the sources (e.g. GitHub) for all Pods are available, CocoaPods is generally able to recreate the same installation. (Technically there is no guarantee that running pod install will fetch and recreate identical artifacts when not using a commit SHA in the Podfile. This is especially true when using zip files in the Podfile.)
There won't be any conflicts to deal with when performing source control operations, such as merging branches with different Pod versions.
Источник
У меня лично в файле .gitignore есть следующее:
# CocoaPods
#
Pods/