Surprisingly slower

gistfile1.txt

static unsafe int CountLines(FileStream file)
{
    var count = 0;

    var vectorSize = 256 / 8; //256 bits, 8 bits in a byte.
    var maskSrc = stackalloc byte[vectorSize];
    var scratch = stackalloc byte[vectorSize];

    for (var i = 0; i < vectorSize; i++)
    {
        maskSrc[i] = Rune;
    }
    
    var runeMask = Avx2.LoadVector256(maskSrc);
    var zero = Vector256<byte>.Zero;
    var accumulator = Vector256<long>.Zero;

    long bytesRead = 0;
    var fileSize = file.Length;

    int read;

    var buffer = new byte[BufferSize];

    while (bytesRead < fileSize)
    {
        read = file.Read(buffer, 0, BufferSize);
        bytesRead += read;
        int i;
        fixed (byte* ptr = buffer)
        {
            for (i = 0; i <= read - vectorSize; i += vectorSize)
            {
                var v = Avx2.LoadVector256(ptr + i);
                var masked = Avx2.CompareEqual(v, runeMask);
                var pop = Avx2.Subtract(zero, masked);
                for (var el = 0; el < vectorSize; el++)
                {
                    count += pop.GetElement(el);
                }
            }
        }
    }

    return count;
}

LineCounter.cs

using System.Numerics;

namespace nlc;

public class LineCounter
{
    public const int BufferSize = 128 * 1024;
    private const byte rune = (byte)'\n';
    private static readonly Vector<byte> mask = new(rune);

    public uint CountLines(Stream stream)
    {
        int read;
        int idxOf;
        int vectorSize = Vector<byte>.Count;
        var buffer = new Span<byte>(new byte[BufferSize]);
        uint count = 0;

        while ((read = stream.Read(buffer)) > 0)
        {
            int i;

            for (i = 0; i <= read - vectorSize; i += vectorSize)
            {
                var v = new Vector<byte>(buffer.Slice(i, vectorSize));
                count += Vector.Dot(-Vector.Equals(v, mask), Vector<byte>.One);
            }

            if(i < read)
            {
                var slice = buffer.Slice(i, read - i);
                while ((idxOf = slice.IndexOf(rune)) > -1)
                {
                    slice = slice.Slice(idxOf + 1);
                    count++;
                }
            }
        }

        return count;
    }
}

Try this

	public unsafe uint CountLines(Stream file)
	{
		uint count = 0;
		var vectorSize = 256 / 8; //256 bits, 8 bits in a byte.
		var maskSrc = stackalloc byte[vectorSize];
		var oneSrc = stackalloc byte[vectorSize];

		for (var i = 0; i < vectorSize; i++)
		{
			maskSrc[i] = 10;
		}

		for (var i = 0; i < vectorSize; i++)
		{
			oneSrc[i] = 1;
		}

		var runeMask = Avx2.LoadVector256(maskSrc);
		var zero = Vector256<byte>.Zero;
		var oneMask = Avx2.LoadVector256(oneSrc);

		long bytesRead = 0;
		var fileSize = file.Length;

		int read;

		var buffer = new byte[BufferSize];

		while (bytesRead < fileSize)
		{
			read = file.Read(buffer, 0, BufferSize);
			bytesRead += read;
			int i;
			fixed (byte* ptr = buffer)
			{
				for (i = 0; i <= read - vectorSize; i += vectorSize)
				{
					var v = Avx2.LoadVector256(ptr + i);
					var masked = Avx2.CompareEqual(v, runeMask);
					var pop = Avx2.Subtract(zero, masked);
					if (!Avx2.TestZ(pop, oneMask))
					{
						for (var el = 0; el < vectorSize; el++)
						{
							count += pop.GetElement(el);
						}
					}
				}
			}
		}

		return count;
	}