実装環境

Unity 2018.3.8f1
Xcode 10.2
CocoaPods 1.6.1

方法

Assets/Editor 下でファイルを生成
(Editorフォルダ内であれば問題ないので、自分はAssets/Editor/hoge/Editor下に置いてます)
実装例

GoogleMobileAdsDependencies.xml

<dependencies>
  <iosPods>
    <iosPod name="Google-Mobile-Ads-SDK" version="~> 7.0">
      <sources>
        <source>https://github.com/CocoaPods/Specs</source>
      </sources>
    </iosPod>
  </iosPods>
</dependencies>

要素について

GoogleのPlayServicesResolverのサンプルより一部参照

SampleDependencies.xml

<dependencies>
  <!-- iOS Cocoapod dependencies can be specified by each iosPod element. -->
  <iosPods>
    <!-- iosPod supports the following attributes:
         * "name" (required)
           Name of the Cocoapod.
         * "path" (optional)
           Path to the local Cocoapod.
           NOTE: This is expanded to a local path when the Podfile is generated.
           For example, if a Unity project has the root path "/my/game" and the
           pod the path is "foo/bar", this will be will be expanded to
           "/my/game/foo/bar" when the Podfile is generated.
         * "version" (optional)
           Cocoapod version specification for the named pod.
           If this is not specified the latest version is used.
           NOTE: This can't be used when "path" is set.
         * "bitcodeEnabled" (optional)
           Whether this Cocoapod requires bitcode to be enabled in Unity's
           generated Xcode project.  This is "true" by default.
         * "minTargetSdk" (optional)
           The minimum iOS SDK required by this Cocoapod.
         * "configurations" (optional)
           Podfile formatted list of configurations to include this pod in.
         * "modular_headers" (optional)
           Set to true to enable modular headers, false to disable.
         * "source" (optional)
           Source repo to fetch the pod from.
         * "subspecs" (optional)
           Subspecs to include for the pod.
     -->
    <iosPod name="Google-Mobile-Ads-SDK" path="../google-mobile-ads-sdk" version="~> 7.0" bitcodeEnabled="true"
            minTargetSdk="6.0">
      <!-- Set of source URIs to search for this Cocoapod spec.
           By default Cocoapods will attempt to fetch the pod specs from:
           * $HOME/.cocoapods/repos
           * https://github.com/CocoaPods/Specs
           -->
      <sources>
        <source>https://github.com/CocoaPods/Specs</source>
      </sources>
    </iosPod>
  </iosPods>
</dependencies>

補足

<sources>タグは必須ではありません
Androidも <androidPackages>を記述する事でライブラリの追加が可能です(とはいえ現在ではGradleを用いた方が良さそう)