$list = Get-MyCoolList
$query = New-Object Microsoft.SharePoint.Client.CamlQuery
$query.ViewXml = "<View><Query><Where>...</Where></Query><RowLimit>4999</RowLimit></View>";
do {
  $items = $list.GetItems($query);
  $query.ListItemCollectionPosition = $items.ListItemCollectionPosition;

  #  ... do cool stuff...

} while ($query.ListItemCollectionPosition -ne $null)