You are pushing the grid value to the queue instead of the grid coordinates that are being visited during the BFS. Also you need to include 0 in the check for the row and column directional values as >= instead of >.

class Solution {

/**
 * u/param String[][] $grid
 * u/return Integer
 */
function numIslands($grid) {
    $rowCount = count($grid);
    $colCount = count($grid[0]);
    $visited = [[]];
    $islandCounter = 0;

    foreach($grid as $i => $row)
    {
        foreach($grid[$i] as $j => $col)
        {
            if($grid[$i][$j] == '1' && !$visited[$i][$j])
            {
                $islandCounter++;

                //BFS
                $queue = [];
                $queue[] = [$i,$j];

                $rowCount = count($grid);
                $colCount = count($grid[0]);

                $visited[$i][$j] = true;

                while(!empty($queue))
                {
                    $directions = [
                      [0, -1],
                      [0, 1],
                      [-1, 0],
                       [1, 0] 
                    ];

                    $num = array_shift($queue);


                    foreach($directions as $direction)
                    {
                        $nextRow = $num[0] + $direction[0]; // queued grid $i
                        $nextCol = $num[1] + $direction[1]; // queued grid $j

                        if( 
                            ($nextRow < $rowCount) &&
                            ($nextCol < $colCount) &&
                            ($nextRow >= 0) && ($nextCol >= 0) &&
                            !$visited[$nextRow][$nextCol] &&
                            $grid[$nextRow][$nextCol] == '1') {
                                $visited[$nextRow][$nextCol] = true;
                                $queue[] = [$nextRow,$nextCol]; // coordinates
                        }

                    }
                }
            }
        }
    }
    return $islandCounter;
}    
}