If an employee is paid on grants outside of my organization, who should certify the effort?

The PI is ultimately responsible for ensuring that all effort reports are certified on their projects. Normally, an effort report can be certified either by the individual or by a supervisor or someone with first-hand knowledge of the work performed. Occasionally, an effort report may require multiple certifications if the individual works on multiple projects, has multiple supervisors and is not aware of which projects their effort is benefiting. In that case, multiple certifications may be required.
Work with the other department to determine the employee’s effort percentage on all projects, as it isn't possible to know what percent of time was spent in one department without knowing the total time spent. Each department should certify only their own projects.